Lost Under Deep Cover
by Koware ta
Summary: AU, Scarlett fails at a mission that causes her more than she initially thought it would. She is broken by Cobra and now under their complete control. Can she break free? S/SE ooc
1. Orders and Commands

AN: I normally don't talk at the beginning but I had to warn readers that this the first time I written for this fandom. I am not confident at all on how it will turn out. I just became a fan in the last week. Snake Eyes and Scarlett is all I ship right now. I have a weakness for good romantic sub-plots. That why I wrote this. As of now it is only a one-shot. If anyone likes it then I will continue. This is **AU** since I don't know where this could take place, and I'm not sure who is supposed to be dead and what time continuity this is. This is more than likely IDW since it's more modern and I'm slightly familiar with what's going on. Sorry if anyone is **out of character**, I just started reading the comics. (I need to lay off the plot bunnies.)

Warnings: Mention of torture and rape.

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><p>Lost Under Deep Cover<p>

I. Orders and Commands

Startling green eyes stared at a wall blankly. The owner of the beautiful eyes didn't even blink when a woman came to stand over her with a smug smile. "Is it complete?" she asked the scientist. He nodded swiftly to the Baroness.

"She should remember nothing but what was programed in to the Synapse Drive. She has had her last relapse. Go ahead ask her." the scientist told Baroness whose attention was on their prisoner. She walked over and looked down at the eyes that held no recognition of the person standing over her.

"What is your name?" she asked the woman who continued to stare unblinkingly. At first the woman on the floor did not answer. She blinked for several seconds and then she sat up and made her way to her feet. "I am Shade, what is my mission?" the woman voice came out crisp and clear. No sign to give away her origins.

"She's perfect. I believe she'll be an asset to Cobra. Get her ready for her next mission. It will be very interesting to see how this plays out." Baroness walked around the woman formerly known as Scarlett with pure glee. Shade would be a great asset to the aspirations of Cobra now that the relapses had ceased. Her last missions cause her to remember things that hindered her performance, but now the memories were locked away permanently, hopefully.

Once Baroness left the room, the scientist helped prepare the woman for her sixth mission. He gave her the clothes she was to wear and briefed her on the mission she was to complete. She stared at the male scientist without blinking. She only gave a replied when one was required.

"Do you understand what you are to accomplish." He asked his experiment and she nodded. He was an ambitious scientist looking to move up the ranks of Cobra. This was his chance, he didn't expect Baroness to give him a chance with his experiment, but she did. This was the first assassination mission for Shade and it was a step forward for him in becoming someone in Cobra. Shade was his greatest creation and he would bring down the GI Joe team with her.

The woman stripped down nude completely unaffected by embarrassment or shame. The hospital-like gown fell to the floor as she dressed in a cocktail dress that was efficient enough for her to use her combat skill if needed, but classy enough to wear to a formal party. She slipped into the five inch stilettos that gave her a height of 5'11. She was given a comb by the scientist. She took it and paid him no mind. The man was short and lanky no threat at all to her.

She continued combing her red locks until he gave her a hair accessory to pull her hair up. She did so without thought. She moved on pure instinct. Once she finished he showed her to a full length mirror so she could fix anything out of place. She stared at the mirror and there was person who stared back. This person was as familiar as a stranger. She didn't know who this woman was, but she supposed it didn't really matter if she did not know. She was Shade. All she needed to do was follow the orders of her superiors. That was what she was created for.

"Go to find a suitable vehicle in the hangar and wait for further orders." The scientist said harshly to her as if he was angry. She ignored his tone because she did not care if he showed emotion. It was not directed to her, so therefore it was not her concern. She left and did as she was ordered.

"Do you really think Shade will be useful, what if she starts remember or one of her former teammates triggers some kind of memory?" the man's subordinate asked.

"It won't work. The device I plant inside of her will suppressed any memories of her teammates and has likely already started erasing her earliest memories. In the next two month she will truth be a shade." The scientist's laugh was befitting for someone who worked in Cobra. His subordinate just stared at him uncomfortably.

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><p>Hawk sat reading over the encoded message sent by one of their intelligence agents. Cobra was planning to assassinate Senator Richard Huntington. He was adamantly against one of Cobra's undercover agency. He planned to shut down all operation, which was a good thing if it didn't put his life in danger. It was a simple mission but he had a gut feeling that some was wrong.<p>

He placed the message down and lean back in the chair he was sitting in. Duke sat off to the side of him. "So who are you going to send?" he asked as picked up the message and read over the content.

Hawk gave it serious thought. There had been a lot active in the past months from Cobra. A lot of the Joes were away on missions. "Clutch, Stalker, Beach Head and Snake Eyes will go." He said knowing that at least two of the four wouldn't mind that much babysitting the Senator for a while. It was a short birthday party. It should be easy. Snake Eyes needed to get out. He hadn't been the same since they lost Scarlett. Well not much changed other than he was unstable at times and isolated himself a lot more.

The guilt ate away at Hawk most days. He had recommended her for the undercover operation. He closed his eyes tightly trying not to think about the missing Joe. It wasn't as if they had not tried to rescue her. The problem was they didn't know where she was. She was only going to infiltrate one of Cobra's affiliates for information, but she didn't return to the extraction point instead she disappeared.

Her communication link was dead and any tracking device in her body was disabled. It didn't take long for Snake Eyes to go to the base looking for her. He had leveled the base in a matter of hours with not one clue to her whereabouts. Hawk was sure that Snake had torture enough people, yet they gave him no answer. Scarlett went missing in January. Snake Eyes leveled the base in November after returning from his own mission, it was now December. Almost a full year and there was no information retrieved on the whereabouts of the Joe. She was declared as MIA a couple months after going missing. Hawk was positive she was in the clutches of Cobra but there was no way of knowing which base. It wasn't as if they had a list of all the Cobra bases.

He stopped his contemplating of that situation and went to call his subordinates to the briefing room. He only hoped that the mission would take Snake's mind off Scarlett for a while. He doubted it but he had to try. He was actually surprised that the ninja had not gone AWOL yet.

Once he finished the brief he looked over the Joes who sat at the table. Clutch looked uninterested with the mission. They really didn't need a driver to protect the senator. Snake Eyes didn't show any emotion. He seemed to accept the mission. Hawk could never tell what the man was thinking. The mask and visor really didn't help either. He made a mental note to take up some body language classes.

Stalker and Beach Head didn't complain per se but he could tell they weren't too thrilled to do something so mediocre. "You're the only one capable of handling this task." Hawk folded his arms over his chest knowing he just told a lie no one believed. Stalker looked over to Snake Eyes and then to Beach Head. This mission was pretty much beneath their ability but orders were orders. "Senator Huntington…huh?" Stalker looked as if he was thinking about something.

"Maybe this won't end up too boring. I'm pretty sure the old man's going to have a couple of desserts there worth looking at." Clutch said already thinking about what kind of women would be at the party.

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><p>Snake Eyes did not see one valid reason for him to accompany them on this mission other than the fact that Hawk ordered him to go. He sighed inwardly to himself. He would complete the mission for no other reason than something to occupy him. He tried his best not to think about Scarlett but he failed. He felt completely useless. He couldn't find anything to help him fine her. He would have gone AWOL at the drop of a dime if he had any idea where she was, but that wouldn't help him.<p>

At least until he actually found something useful on the whereabouts of the female Joe. For the time being he remained idle which was something he never did. He still was unsure why he hadn't searched out other Cobra bases and tortured every person there until he got the answers he wanted.

Oddly, he knew that if he stayed with the Joes he'd find her faster. Although remaining with them for almost a month since he returned and was told she had went missing, still nothing had turned up. He could feel his patience growing thin. He clenched his fist tightly. He hadn't signed a word since he was told she was missing. It wasn't deliberately he just didn't feel the need to say anything to anyone. He stayed even more to the shadows and out of sight, lest he took his aggression out on someone.

He sat atop the roof of the Senator's house out of sight watching the guest stroll in. He had a feeling that tonight would be boring to say the least. He continued to watch for anything that was suspicious but saw nothing but civilians. No one had any quirks that caught his attention or had body language that showed ulterior motives.

Hours passed by uneventful as more people poured into the three story mansion. Snake Eyes let his mind wander back to the day just before Scarlett left for her mission. He didn't want her to go so unprotected. She was practically on her own when she got inside, which was what bothered Snake Eyes. He couldn't help her once she was inside. It wasn't that he didn't trust her skills but the fact was that he would be too far away to help her.

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><p><em>*I don't like this* he signed to the redhead. She was looking at the suit she was supposed to wear. It was a standard issued uniform for the base she was going to infiltrate. <em>

"_I know." She said looking at the tag for her ID. "But there's no one else who can do this. Hawk thought I was the best choice and I am. I can handle myself you know." She tied her hair in a knot and picked up some training clothes. She never minded when he visited her in her room, which she could count on one hand how many times that had been._

_He had closed some of the distant between them in the few years they had worked together. She was still jealous over him choosing Helix over her but she trusted him. They worked together on mission, she had to admit that, but it disappointed her. Most days she felt the need to prove herself to him so much so she'd take mission that were high-stakes, like the one she was taking on in a couple of days. _

_*I know you can take care of yourself but you have no back up. I won't be able to help you.* his worry showed in his signs. She thought about what he said. It was true. He would be on another mission for a couple of months and no one else had his stealth skills to navigate through the security grid that the Cobra base had._

"_You worry over nothing, I can handle this. Just you wait, when you return I'll be here waiting for you instead of you waiting for me. We could even wager on it." She tried to lighten the mood and assure Snake Eyes that she could handle it. They weren't in a relationship and they didn't exactly have a name for what they had between them, but they were close and his worrying over her made her unhappy. She just didn't want him to be anxious over her, when he had an important mission as well. _

_*Just be careful.* he turned to leave not in the least relieved. She stopped him before he put the mask on. She kept her quarters dark for him. He was self-conscious about his face and really who wouldn't be. She hesitated slightly. She didn't know what she was doing. Things had been shaky for them for a while but now thing were finally smoothing out. She didn't want to ruin it, so she let his hand go and looked at the floor. _

"_I'll be careful. I promise." She gave him her best reassuring smile. He only nodded to acknowledge her. She could tell he wasn't at all relieved though._

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><p>Snake Eyes hadn't even realized that he had slammed his fist against the shingles of the roof. A couple of them where broken. He lifted his hand up and clenched his fist. He wouldn't wait much longer. If nothing turned up soon he would find her on his own. He sat quietly on the roof and continued to watch the guess pull up to the mansion in their expensive cars.<p>

One car caught his attention, only because of the attention the crowd was giving it. It was Mercedes-Benz SLR McLaren, candy apple red. It stopped at the valet who waited. The scrawny young man opened the door. The first thing out of the car was a red platform stiletto and then came the owner of the leg.

Snake Eyes couldn't see the woman's face since she kept her head down, but he knew who she was. He knew that shade of red hair. He moved across the roof silently to get a better look.

"Check out Poison Ivy." Clutches voice came from the communications link. "I can't see her face though." He said. The red head woman continued toward the mansion looking down to the ground. Once she was close enough to the mansion she stopped walking. The red purse she carried slipped from her hand. She gracefully bent over and picked up the small item and tucked it under her arm. Then she looked around with an embarrass smile. The guests seemed to forgive her blunder and continue with walking to the mansion.

Clutch saw it first from his stake out position. He blurted out her name loudly across the comm link. "Scarlett!"

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><p>Shade smiled at the guest sweetly. She needed to fit in, so she went for dainty. She looked around at her surroundings. She was told that the senator would have bodyguards that were unseen. She easily took that in to consideration by scanning the area looking for anyone who seemed too serious. She found none. She continued up the walkway to the mansion, she made sure her walk caught the attention of the men around her. It was unneeded attention but having admiring eyes could come in handy.<p>

She stopped and lightly ran the tip of her ring finger to the side of her mouth as if she was getting lipstick from the corner of her mouth. She wasn't, her communication link was embedded in the tip of her ring finger. "Now commencing with my mission." She said lowly, when she finished she dropped her hand and found her an escort. She slipped her arm under a larger man's arm, who was a guest.

"Miss?" he was confused at first but her smile was disarming. She gently ran her fingertips over his bicep that was cover by his suit.

"I came alone tonight and well you seemed as if you were alone too. I just don't want any of these men hitting on me. Would you mind being my escort for tonight?" she pouted lightly for the effect. The man like any other nodded and agreed to be her escort. Who was stupid enough to reject a woman's advance that looked like that?

She found herself staring at the roof of the mansion. She supposed it was a great hiding place for some who wanted to watch the crowd. Not many people would look up there. She settled her eyes back to the mansion as she walked the flight of steps to the door.

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><p>"What the heck is she doing here?" Stalker whispered across the comm link. He wasn't expecting an answer. He moved up the steps behind the woman and her escort. She hadn't seemed to notice him and if she did she showed no signs.<p>

He casually bumped into the escort who looked at him. "Pardon me sir." Stalker said to the man. He kept his eyes on Scarlett's reaction to seeing him. She didn't seem to react at all. She just smiled at him with no recognition.

"It no problem at all, is it darling." She asked the man whose arm she held. He shook his head and gave a quick no, completely interested in the deep green cocktail dress Scarlett was wearing.

"It's so crowded here that I'm sure everyone is bumping into each other." She laughed. Stalker was positive that Snake Eyes was losing it wherever he was. This person in front of him was not Scarlett. She looked like her, but her personality was nothing like hers and she didn't have the slightest southern accent.

Stalker stayed a few feet from Scarlett and kept an eye on her. Beach Head kept an eye on the Senator, while Clutch was outside letting Hawk know what they were encountering.

Snake Eyes watched from a different position. He wanted to grab her to make sure what he was seeing was real. Scarlett was there as if nothing was wrong. No injuries or anything of the like, but he could tell something was off. She didn't react to Stalker at all. He was like a complete stranger to her.

He had a feeling that she was the assassin. There was no other reason for her to appear in such a place. He could care less about the mission now. He needed to get to Scarlett.

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><p>Shade dance on the floor with the escort and then made her way to the Senator, effectively leaving the escort with a couple of admiring women to keep his attention. The Senator was a tall man who was in his early fifties. She seemed to catch his attention without trying. "Have we met before?" she asked him.<p>

"No, I think I'd remember a hair color like that." He said shaking her hand then introducing himself. It didn't take her long to charm the Senator. He was more than ready to ditch his own birthday party to get to know her better.

"You should at least wait until your blow out the candles." She leaned into him and smiled. He nodded in agreement. He couldn't wait to unwrap his present at the end of the night. She was used to doing this kind of charming.

Elsewhere Snake Eyes watched trying not to kill the Senator with a throwing star to the neck. He didn't want to think about the lack of self-control he had for just contemplating doing that. Scarlett's action was proof that she was the assassin and it didn't surprise him at all. Cobra would use anything means necessary to accomplish its goal. It was better than the alternative things that they could have done to her.

He had to wait until she got the Senator alone before he could make his move. For the time being he had to watch Scarlett flirt with the man. It bothered him more than he would have liked. He understood his feeling for her and had even become closer through much trial and error, yet he still wasn't sure on how to act on those feelings. He wasn't exactly the ideal lover.

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><p>As soon as the guest cleared the room and left Senator Huntington was leading Shade to his bedroom. She followed quietly behind the man through the darken hallway. She held his hand with one hand, while sliding her other hand between her cleavage. She grasped the small knife and pulled it out. The senator got to his bedroom and was about to open the door.<p>

Shade quickly went for the Senator's neck, but pulled back abruptly. She looked at the throwing stars in the wall and then scanned her surroundings. The senator had fallen back in to his room scrambling to get away from her. Her attention left him quickly as more of the sharp stars came at her. She dodged by dropping to the floor. She quickly got to her feet and went for the senator but was stopped by a blade in her face. She backed up, and turned her attention to owner of the blade.

Shade was taken aback by the mask. She quickly moved back further. She didn't understand the fear she felt. She had never met this person, but she was fearful. He didn't move nor did he speak he just stood there. Shade was unsure of what to do. She was only ordered to kill the Senator. No orders were given about interfering parties. She needed orders. She could not function without them. None were given to her even as she stood there with indecision.

Shade continued to stare blankly at Snake Eyes. He hadn't moved a muscle only continued to watch her. The senator remained quiet. He was only glad that his life was saved. Snake Eyes grabbed the doorknob without taking his eyes off of Scarlet and closed it with the Senator inside the room.

He was unsure of what to make of Scarlett. She stared at him with no recognition. Staring into her blank eyes told him all he needed to know. She was brainwashed. He needed to capture her if he had any hopes of finding out what happen to her in the last elven months.

Shade continued to watch the ninja. She moved her hand slowly upward, but before she could even as for orders the ninja was coming at her. She attacked out of instinct, which he easily evaded. She realized he was faster than her, but she continued to attack. He blocked every move she made.

She was quickly being cornered. Capture was unacceptable that order was given without words. She abruptly turned from the ninja and ran. She looked back and he was already gone. As soon as she turned he was there, she could barely stop herself. She did though, just short of his arm reach. She quickly grabbed the small caliber pistol she had between her thighs.

She only needed a distraction as she unloaded all but one of the bullets at the ninja. He quickly dodged and sprinted at her while doing so. Shade didn't see a way out. She quickly turned the gun on herself which cause the ninja to stop sharply. She was confused by his actions. She stepped back slowly, yet he still followed slowly.

"You will not capture me." she didn't hesitate at all. Snake eyes could tell she would do what was necessary not to be capture. He couldn't get any closer, but he couldn't let her get away either. Shade's attention was fully on him as she backed up. Her green eyes stared at the black mask. Before she knew what was happening the pistol was knocked out of her hand and she was tackled to the floor. She tried to move but she couldn't, two people were holding her while the ninja came over. Before she knew what was happening everything faded to black.

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><p>Shade opened her eyes to a blinding light above her. She lay on a metal bed without moving. "Understood." She said out loud to herself as she received her order through the interface in her brain. She sat up and inspected her surroundings. She was in a holding room. Her orders were to return to the base by any means necessary.<p>

She looked down at the clothes she was wearing. It was nothing but a gown. She had no weapons or any way of escaping until someone entered in the room.

Snake Eyes stood outside of the room with Hawk and Duke. What they had found was disturbing to say the least. "I call for a neurologist. Some of our medical technicians informed us that there was something abnormal about Scarlett's MRI. Something none of them is familiar with. " Hawk said looking at Scarlett through the glass window. She had just awakened. She was looking around and spoke to herself which caught Duke and Snake Eyes' attention.

"She's receiving orders." Duke said. Snake Eyes quickly left the room and entering the holding room. Scarlett looked at him and quickly attacked, throwing her body though the air at him. He caught her foot before she landed a blow. She went for a punch but was also stopped. He realized that she wasn't fight at her full potential. It was as if she didn't know how. Her moves were smart but lack ferocity. He knew for a fact she could do better. He threw her back toward the bed and grabbed her hand holding her down with his weight. He looked at her right finger easily noticing the different in her fingerprint. It was a surgical scar, tiny and almost insignificant. Duke gave Snake Eyes a small pocket knife. He proceeded to remove the comm link from her finger. She said nothing as he cut into her finger she just remained still. She could probably receive orders but not relay anything else.

Shade watched as another blonde haired man entered the room. The ninja finally go off of her and she sat up looking at her bandaged finger. Her attention went to the man who entered. He had and air of superiority around him as if he was in command. He stared at her as if he knew her.

"You want to interrogate me?" she said looking at the other blonde that was also staring at her as if he knew her. She found no use in trying to escape with someone far more skilled than she was in the room. She glanced at the ninja.

"No Scarlett, I'm not here to interrogate you." He said folded his arms over his chest while Snake Eyes moved to the corner of the room. He observed her while Hawk continued to converse with her. Her attention moved to the ninja. He was a threat.

"Scarlett? My name is not Scarlett. I am Shade." She said but hesitated slightly. She stared unblinkingly at Snake Eyes until she looked to be in a trance.

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><p>"<em>Hello Scarlett, or should I say Shana?" the voice that spoke was unfamiliar to Scarlett. She didn't respond to the question. She had to control her breathing. They knew her real name, with that they could find her family. They would kill them. She could feel herself starting to panic, but she held on. She couldn't allow them to know that was a weakness for her. They would torture her with that.<em>

"_Do not worry too much. We're not going involve your family in this." He said. She didn't show relief at him telling her this. She wasn't to show any emotion. "Just like a good soldier." The man said as he came into view. He was wearing a white lab coat and had an assistant beside him. _

_Scarlett looked around herself. She was restraint to a metal table. The only thing that covered her was a thin sheet. She was freezing but that was unimportant. She tested her binds even as the scientist spoke to her._

"_You see you're my chance to impress the higher ups. I'm not going to waste this once in a lifetime chance with useless threats. I'm going to break you. Then I'm going to take away everything you care about without kill anyone." He tapped her forehead with his index finger. "All I have to do is rid you of those memories." He smiled at her. _

_Scarlett felt her heart sink, but she was taught never to show weakness even if it was her last breath. She said nothing to the man who stood over. She didn't even look at him anymore, instead she focus on remaining calm and detaching herself from the situation. It wasn't the smartest thing she could do, but at the moment she was sure she needed to do so._

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><p>Shade didn't respond to the question Hawk had asked her. She continued to stare blankly at Snake Eyes. He continued to watch her knowing that she wasn't aware of anything but whatever was going on in her head. Hawk moved closer the woman who sat completely still.<p>

She mumbled to herself. Everyone listen but her words seem almost incoherent. Words like orders, duty and mission spilled forth in sentence that were like a mantra. She slowly rocked back and forth while chanting. "Orders take precedence." Scarlett started to unravel in front of them.

She stood abruptly and looked at each one of the men in the room. "Commencing mission." She said to no one but herself. She attacked Hawk who was behind her at first. He side stepped her first attack, but she landed the second, which was a swift kick to the groin. He was expecting such dirty tactics. He tried to prevent himself from doubling over but the pain was too much.

"General Hawk?" Duke called as he tried to take her from the back. Shade turned in time to avoid his tackle. Snake Eyes could tell she was going at her full potential now. She was like at cornered animal attacking anyone who was a threat. He didn't help Duke; instead he continued to observe her while they fought. She pulled no punches, while Duke did slightly. She used her feet expertly as she blocked Duke's punches with her forearms. It was an interesting fight to say the least until Duke gained the upper hand by grabbing her leg and yanking her forward.

She was caught off guard and fell forward on to Duke. "Been a long time hasn't it red." He said as if she was supposed to know what he was talking about. Shade didn't like the tone he used. It was too familiar to her. She tried to blind the blond Joe with her index and middle finger. He pulled back in time and she turned the eye-poke into a punch. She hit him dead in the nose effectively breaking his nose and temporarily blinding the arrogant overly familiar fool.

Shade was shocked by her thoughts and anger. She wasn't order to care about such things. She turned to the ninja who still hadn't moved. He just observed her with cold calculation. "I-I am…" she wasn't sure what she was supposed to say. She didn't want him to think she care about the blonde. He'd have to have known that she did care for the blond from the moment she broke his nose without a second thought.

Shade shook her head as her thoughts jumbled. Why did she care about what Snake Eyes thought? Snake Eyes? Why did she know that name? She stumbled away from the two men who were getting up. Her thoughts were not important. She had to follow orders. Nothing else should concern her except for commands that were given. She suddenly screamed in pain as what felt like fire traveled down her spine and electricity through her brain.

The pain exploded in her head with enough forced to send her staggering back into the wall. She could hear her superior screaming at her to obey but she didn't want to. She didn't want to be weak in front of him. She could feel something against her spine. It was under her skin causing her so much pain. She grabbed her head in excruciating pain. She was taught to obey, yet she couldn't. She didn't want to.

"Someone please, help me!" she cried out and the man who had stood silent was by her side before she could blink. Blood leaked from her eyes and nose as the pain became blinding. Shade screamed out in agony as she felt like her insides were on fire. She tried to claw out her own throat, but the man who was by her side stopped her by grabbing her wrist.

He couldn't let her continue on so he knocked her out. She went limp in his arms while. Duke was trying to get a look at her and keep himself from bleeding all over the floor. Hawk opened the door and let the medics in. The interrogation wasn't broadcasted like they had with Scarlett the last time. This one was private. Hawk had made sure that medics were waiting outside Scarlett's room like guards just in case she had tried to suicide again.

Snake Eyes sat in the room alone with Scarlett after Duke and Hawk had left. All he could think about was the anger she showed when Duke had spoken to her. She then looked so scared, when she looked at him. As if she was afraid of disappointing him. He already knew of her and Duke's former failed relationship. It was one reason he tried to keep their relationship platonic. He knew Scarlett's feeling for him, but he wasn't ignorant about his looks versus Duke's. A blind person could tell who would be the better choice.

She was deeply sedated and probably in an induced coma until the neurologist got there. Snake Eyes stood up and left the room he went to meet Mainframe. The man sat at a computer hacking into the microchip he took out of the comm link from Scarlett. He looked up the ninja. "I know, I know. I'm working as fast as I can. This is pretty complex. Nothing I've seen before." He said turning back to the computer screen.

Snake Eyes stood off to the side looking at different things. Mainframe stopped for a minute and looked back at Snake Eyes. "You're hovering." He said.

Snake eyes looked at him but that was all. Mainframe sighed lightly and then went back to work, while under intense pressure from the idle ninja.

* * *

><p><em>Scarlett sat looking at the wall in front of her. She had her fist slightly in her mouth so she wouldn't cry out. She was breaking. She was breaking quickly. She hadn't slept in what felt like weeks. No windows to tell her the time, nothing but the freezing temperature of the room that fluctuated between extreme hot and cold.<em>

_The torture had started out light, poison that wouldn't kill at the small dosages. She was sick for long period of time and that was bearable, but then came the insomnia. They wouldn't let her sleep. Noises persisted every time she was close to sleep, always when she was so close to being fully sleep. _

_She was unsure of how long it went on, but after a while she had fainted from sleep deprivation. That neither was long lived as the scientist pumped her veins full of adrenaline. The beatings began shortly afterwards. She was held down and beaten by Cobra grunts and even Baroness had fun making her bleed. She had broken bones and deep cuts in her back, but no wound were ever in places like her legs or arms._

_From there she was moved to actually torture. From dry drowning to electro shock she endured it without breaking, but now she sat in the small room breaking down from the last torture. Being violated was the last straw in her sanity. She felt dirty and there was no cleaning it. She wanted to carve out her own guts as she remembered the filth she had been touched with. Then there was humiliation of being watched by several others as well. She couldn't recover mental from the tortures because she wasn't ever given reprieve. At that very moment she was so tired she could have fainted but she was full of adrenaline. _

_Scarlett knew she didn't have much time left. She needed to get a message to the others but she was unsure as to how. She was in a locked room with no one allowed in. She felt the helplessness sink in. She was going to give in soon and wasn't going to be by choice. She could barely think straight anymore. All she wanted to do was curl up and die but that would not happen._

_The door opened and the man that had at some point introduced his self as Puppeteer entered the room. In his hand he had a syringe and with him there were four men. "Now, now Scarlett, I think it time we get to the actually breaking of your psyche. All this up until now was just the entrée." His smiled was what gave her nightmares and she could do nothing but fight futilely. She screamed and fought the men who held her down and it was all useless in the end because once the syringe was in her back she was unconscious, helpless to do anything._

_When she had awakened she was on a metal table. She tried to sit up but the pain in her lower abdomen prevented her from doing so. She couldn't move. Her back though was worst. The pain felt like her spine was on fire. She could feel it all the way to the base of her head. She screamed in frustration. _

"_Good morning Scarlett." The puppeteer said laughing lightly as he stared down at her. "I'm surprised to see you've awakened after such rigorous surgery. Performing a hysterectomy was interesting slightly, but attaching the Synapse Drive to your brain and spinal cord was much funnier." He tapped her abdomen sending shockwaves of pain through her body. "You'll be used for the rather dirty jobs, so we can't have any little surprises running around. Even I didn't want to go that far, but hey, it's for the better."_

_Scarlett anger brought her body off the table but the restraints kept her in place as she screamed. "I'll kill you, I'll kill all of you!" she bucked up and fought the restraints even though they cut into her wrist. She could feel the tears as they sprung to her eyes and leaked down her cheeks. She screamed until her throat was raw._

"_What an ill display for a soldier. It's fine no one outside this room will ever know you broke down so badly." The puppeteer walked away from the metal table and stopped at the door. "You will not have to worry much longer. Soon you won't worry about anyone or anything anymore." He said as he left the room._

_Hours passed and soon Scarlett could hear the voices in her head. Orders. She was being given orders, orders that she was compelled to follow. She was told to forget her past. She was commanded to forget her life as Shana and Scarlet. She was to become a blank slate, to obey, to never question the orders given. She was to become Shade. Scarlet was to fade away. _

"_No…" Scarlett cried out. Her thoughts were failing against the programing of the Synapse Drive. She was succumbing to the device. She didn't know what it was but it was destroying her mind. She had to stay strong. She had to because she wanted to see him again. She wanted to be with him. Who was it that she wanted to stay strong for? Scarlett panicked as his name eluded her. "No!" _

"_My name Shana O'Hara… I am- I am Shana…" she cried out. "I am Shana…Shana…" she could remember what she was doing there, but she continued to say her name. "Shana… I'm Shana…" she gasped out as the pain in her body heightened. "I-I…am…sh…sh…-" her voice broke as tears slowly ran down her cheek. Her face became blank as her memories were locked away. _

"_I am Shade. What are my orders?" The woman asked waiting patiently for her commands._

* * *

><p>Shade stared blankly at the bright light above her. Her hand went to the scar on her abdomen. Tears rolled down her cheeks and dripped on to the sheet of the bed. "I need orders…without them…I –I don't know what to do." her voice broke the silence of the room. "I am…Shade." She said unsure of herself. "I am Sh… sh… Shade? Right? I am Shad- …Shana?" the distressed woman cried out in pain.<p>

The dream was real and she could not ignore the effort that she had put forth not to completely lose herself. Shade didn't ignore the name. She embraced it. "I am Shana…" tears streamed her face as she said it louder. That was her name and she knew it like that back of her hand.

"I am Shana!" she screamed out despite the pain that wanted her forget that fact. She wouldn't succumb to it. "I am Scarlett!" she cried out slamming her hands into the bed. "I am Shana, I am her that is who I am…" she smiled to herself as blood came from her eyes and nose. Medics filled the room but she fought them as they tried to sedate her.

"Please, I'll forget if you do this. I know I'm Shana O'Hara. Please don't do this. I don't know anything else but I know I'm Shana, I'm Scarlett. I don't want to forget…" she swayed a little.

"Don't Sedate her." Hawk said entering the room. "Leave her alone. We don't know the consequence if we do sedate her." the medics moved away and gave her some space. One of them gave her a sterilized cloth to clean her face with. The medic asked Scarlett if she wanted a mild anesthetic to which she told the medic no.

"I don't know anything else." She wiped the blood tears from her face. "When I try to grasp at memories I'm assaulted with pain. I don't know anything other than my name because that's what I had chanted in my dream. You called me Scarlett. I only vaguely remember that but Shana I remember." She stared down at the bed. "I'm sorry to have hurt you earlier."

Hawk could tell she wasn't lying. He never did tell her, her true name. "It's okay." He said looking at the lost look on her face. She nervously pulled at the end of her gown. "Something is bothering you?" he asked her knowing of course something was wrong.

"There is a kill switch built in to the Synapse Drive. The puppeteer should have already used it." she looked at the General.

"While you were asleep we installed an electromagnetic field in this room to prevent any kind of contact between you and Cobra. You're safe." he said glad that they had erected the field. Scarlett would no doubt be dead if they hadn't.

"For now…" she said looking at her shaking hands.

"Huh?" Hawk said not hearing what she said.

"I'm safe... for now. He'll find a way. He always finds a way to break me." she said wrapping her arms around herself.

* * *

><p>AN II: Sorry if it's really long. I'm also sorry if any of the characters are weird. I don't have the personalities down yet. Except Scarlett who personality has to be weird for a while, hence the way she talks. I read some of the marvel comic and I like Snake Eyes personality but the IDW one is more aloof and mysterious. So I tried to write him like that. Which I'm pretty sure I failed at. Review if you want.<p>

~.^ ^.~


	2. Replase

II. Relapse

"10…9…8…" Scarlett counted off backwards as she stared at the white ceiling. Medics stood over her as she counted, watching as she slowly drifting off to sleep. Once Scarlett was unconscious the neurologist moved to stand over her and gave the medics the 'ok' to turn Scarlett over. The doctor was tasked with examining the device that was attached to Scarlett's spinal cord and to the base of her skull.

It was a tedious job. He was unable to use heart monitors or any kind of electric medical equipment. The only things he had were a light and any medical equipment that didn't require electricity. Apparently the patient needed to be kept under an electromagnetic field at all times. Kill switch. The neurologist was familiar with those from his career in the military. He was used to being pulled off duty for certain military issues. It was normal for him, but when he had opened the woman's it was anything but normal.

He advised all of his assistants to stop what they were doing. He moved closer to inspect the device attached to her spine. The device had a titanium shell preventing any kind of rejection from body. He took his light to look at each side of the device. He requested that an assistant write down his observations. He continued examining the device, careful not to touch it too much.

* * *

><p><em>Scarlett stood with her legs separated and her hands against a cold wall. She had failed to complete her second test run, so she was being punished for disobedience. She flinched as the whip came down against her flesh. It slashed through her flesh repeatedly. She said nothing, not even a whimper escaped her mouth as she received her beating. <em>

"_You understood your mission and yet you failed. I told you to bring me the information on the strike team. You brought me nothing!" Puppeteer screamed at her from where he stood a few feet away. His subordinate stopped beating her and looked toward his boss._

"_Sir…she's losing a lot of blood." The younger man said. A hint of worry laced his voice. _

"_Don't stop. Shade has to learn that failure is not acceptable. There is no room for mistakes here. Beat her until she drops!" the scientist started to pace back and forth. The younger man hesitated and looked between Scarlett and Puppeteer._

_She didn't look at him nor did she acknowledge his presence. It was as if she was in the room by herself. The only evidence that she was even aware of anything was her slight recoil from the pain._

_Only after Scarlett had went down to her knees did the beating stop. She sat on the white floor staring blankly at her blood. "Orders should be followed. Missions should always be completed. The superior's commands take priority." She chanted to herself as a medic came in and began to tend to her back._

_When she was properly bandaged she was released from the torture room. She traveled down the hallways of the base. Her eyes were fixed on the floor as she traveled to her quarters. She stayed in one of the smaller facilities under Cobra. It was mainly for scientist who did various experiments. A large amount of Vipers occupied the base as well. With the number of intelligent scientists gathering in one place it was important to guard them._

_Scarlett finally reached her quarters and sat down to a table. Her room was bleak like her existence, white walls that matched the floor. Inside there was a metal framed bed, a metal table and chair. She was only allowed to use paper and pen. She unsure as to why she wasn't allowed around electronics, but it was an order she was to follow. She sat looking at the pad and pen. She picked up the pen with her left hand and started to scribble on to the paper. At first it was just mindless writing. Then she started to doodle._

_First she drew a rectangle. She stopped and search for a red pen. After finding it, she used it to shade in the rectangle carefully. Then she drew two smaller rectangles beneath the large one. She shaded each rectangle; and proceeded to draw another larger rectangle below those two smaller ones. She shaded that one in as well. She repeated it until there was six rows of rectangles, alternating between full rectangles and two smaller ones. _

_She was fascinated by her work. She tilted her head as realized she had it upside down. She turned the paper correctly, so that the two smaller rectangles started the pattern. She smiled to herself and stared longingly at the pattern. She continued to look at the pattern until tears steadily streamed down her cheeks. She pressed her face against the sheet of paper wetting it with her tears. _

_Scarlett didn't know why looking at the pattern made her so emotional or why she felt so lonely. She was not ordered to display such emotions and doing so was a violation of the rules that her superior, Puppeteer, had given her. She quickly sat up knowing the punishment for disobedience. Puppeteer showed no mercy, even if he had already beaten her, he had no qualms in dealing more pain to her if she was being insubordinate. She quickly shredded the sheet of paper into tiny pieces. Looking at the tiny pieces that laid in front of her, she began to cry against her will._

* * *

><p>General Hawk sat at his desk listening to the neurologist, who had just finished examining Scarlet. He waited as the doctor gathered his notes. Once the doctor finished Hawk gave him permission to proceed.<p>

"I have no idea what I'm dealing with. The device is fused to her spine. I can't just take it off without knowing the consequences." He said reviewing his notes and showing pictures of the device to Hawk.

The general looked over the pictures. It seemed like an impossible feat. He dropped the pictures on to his desk. "Wait." The doctor said. He looked up at the neurologist. "I was able to deactivate the trigger for the electric pulse that would have killed her. Strangely it wasn't attached to the other device. I've also checked for anything other surprises. It also became apparent that the device can only affect her mind and send small electric pulse to cause pain. Otherwise she is safe for now." After speaking neurologist gathered his papers together he had strewn across Hawk's desk.

"There is one other thing I suggest." The doctor said placing his papers in a folder. Hawk waited for the man to finish his thought. "She should be given a full physical exam. I'm not a general physician but I do know that some of the scars I encounter should be documented." The man stood waiting for Hawk to let know what he should do.

"Thank you, Doctor. There is one thing I need to as you." He said as he shook the man hand. "Do you think the device can be removed? I mean is it possible?" he asked.

"Yes it is, but not by me or any other doctor I'm acquainted with. I'm positive that the only person who can remove this device is the person who attached it. Anyone else is would be going in blind and could end up hurting your soldier a lot more than she already is." The general nodded to acknowledge the man and then dismissive him, having Cover Girl also relieve the doctor of any data from the examination.

After he finished with the doctor he called for Psyche-Out. He was going to need his secondary expertise.

* * *

><p>Meditation was supposed to be relaxing for Snake Eyes, but lately he couldn't seem to concentrate long enough to clear his mind. Scarlett was safe but she had endured a lot. He was only slightly relieved by her being back safely in the pit. From his observations he could tell her emotions were mute. She acted more like a doll than someone who was brainwashed.<p>

Seeing her breakdown emotional, only made him want to find the sad excuse for a human being that had done that to her, but current they still had no leads. His patience was once again being put to the test. Mainframe was worked on the communication link they retrieve from Scarlett non-stop for almost two days without any clues as to where it came from.

He wanted to see Scarlett. At least check up on her, but she was prohibited from visitors. It was understandable she wasn't exactly non-threatening, at least not to the others. He stood up from his meditation pose. He wasn't getting anywhere.

He pulled on some black clothes and grabbed his mask and visor. He was going to see Scarlett. There wasn't any problem as long as he wasn't caught, which obviously wasn't going to happen. He opened the air vent in his room and pulled himself up.

He traveled through shaft stealthily. When he reached the room Scarlett was placed in he saw that she was lying on the bed asleep. He decided he wouldn't stay long, just enough to make sure she was okay.

* * *

><p>Scarlett opened her eyes to a different white ceiling, than one she had fallen asleep looking at. She wanted to move but that wasn't an option. She realized after a minute she was actually staring at the wall because she was on her stomach. She blinked a couple times to clear her vision then continued to stare at the wall for several minutes until she heard the door open. She didn't move to see who it was. She didn't care at the moment she hurt too much to move unnecessarily.<p>

"Good morning Scarlet." The voice was very familiar to her but she couldn't place it to a name or face. She moved to see the face of the man who spoke to her. She got no reaction from staring at his face. She didn't know who he was, just another medic to her. "You shouldn't move. You'll tear your stitches."

"You're familiar." She said finally voicing her thoughts. The man gave her a gentle smile.

"I'm here to check on you. My name is Lifeline." He said to her and realized she still didn't know who he was. "It's okay if you don't remember just yet." He checked her blood pressure and her attention stayed on him for the length of time that he was near.

"Can I have a pad and pen?" she asked wanting something to do other than stare at the walls.

"I'll see what I can do." Lifeline said as he checked her stitches. Once he was satisfied none had broken he left her to find out if she could have a pad and pen.

Once the man returned he gave her the pad and pen she asked for and she thanked him. After he left she pushed herself to sit up and gently leaned on the pillows with the pad and pen in her lap.

She glanced up at the air vent across the room. It was a perfect for escaping or watching someone. She almost started to open the pad but she looked at the vent again. Her back ached but the vent had gotten her attention.

She didn't feel like she was being watched or anything other than the cameras in the room, but she felt like something was up with the air vent. She shrugged it off and opened the black note pad. She was used to writing on lineless paper and was a little disappointed with the college rule in front of her. She doodled for a while.

She got off her bed and left the pad there and went to stand under the air vent. She wasn't supposed to get up but she wanted a closer look at the vent. She didn't see or hear anything suspicious, but she knew someone was in the air vent. She wasn't sure why she knew someone was there.

"Do you know me too?" she asked out loud but receive no answer. She didn't say any more after her question and went back to her bed. After hour of doodling another man entered the room. He didn't look like a medic or as if he was there to check her vitals. She became attentive to the man's every action. She gasped the blue pen ready to strike if provoked.

"I'm not here to hurt you." He said as soon as he noticed she had gone into defensive behavior. "I'm Psyche-Out. I'm just here to talk to you." He took a seat in a chair off to the side of the bed. Scarlett relaxed her muscles some because the man didn't seem hostile. She was still wary of him but picked up her pad and pen and resumed drawing.

Psyche-Out observed her for a bit, watching as she slowly relaxed. She ignored his presence and persisted in her drawing. "I had no idea you were artistic." He tried to get a conversation started. She shrugged at his comment and basically ignored his presence again.

"Could I take a peep?" he tried again. She looked at him hesitantly. She passed him the pad and he looked at her small drawings. First it was meaningless circles. Then little heads of cartoonish characters. Each one had three dots under the head. One of them had a striking resemblance to Snake Eyes. He had to prevent himself from laughing at it because it was so crudely drawing but he could tell automatically who it was supposed to be.

Under the head it had three dots then 'Snake Eyes?' was written beside the three dots. As he continued to look at the doodles he saw one he had seen before. It was a pattern he had seen on the blade Snake Eyes used. "This is pretty well drawn." He said smiling at her. "You remembered your teammates' most prominent features." He noted to himself her surprise.

"These are people I knew?" she asked. He nodded to her and she took the pad looking at the doodles. "People I knew…" she looked at the man who sat in the chair observing her. "What do you really want? I don't know anything about myself, so what reason is there for a psychiatrist to talk to me?" she asked perceptively.

"That is very true but you do have memories." He said.

"Yes. I remember everything from the moment I woke up." She looked at him wondering what was so important about her memories.

"Tell me about yourself. What did you do?" he asked her and noticed she seem less wary.

"I completed my mission. If I had a relapse I would be beaten. I was to stay within my domicile unless I was called. My meals were brought to me. Pad and paper were the only items I was allowed to use." She started to fidget slightly.

"Relapse?" he waited for her to explain.

"I would freeze up. I couldn't focus. I would not finish the mission or I would get hurt because I froze. I was shot once because I froze up." She fingered the scar on her shoulder.

"What happened when you returned?" he asked gently pushing her to continue.

"I don't know. I assume I relapsed further to the point that Puppeteer had to activate the Synapse Drive at a higher setting." Her eyes drifted to the wall and her focus left Psyche-Out.

"Scarlett?" he called. She didn't respond. She seemed to be lost in her thoughts.

* * *

><p>"<em>Orders take precedence, Commands are priority." Scarlett repeated over and over. "Disobedience shall be punished." She chanted repetitively as she sat in the small white room. She rocked back and forth trying to clear her mind. <em>

"_Her relapse is worst then before." The young man tried to calm the woman down who was bleeding all over the floor. Puppeteer stood at his computer console ignoring his assistant and the chanting that got louder. _

_Scarlet started to cry out loudly as the device started to activate at the higher level. Her scream was chilling. The man who tried to calm her moved away as she started to thrash. "My head!" she screamed slamming her head into the wall violently. "Take it out!" tears streamed her face as her memories she had slowly grasped shattered to pieces again. _

"_I'll kill you…" she swore to Puppeteer._

* * *

><p>Scarlett came to being dragged away from Psyche-Out. He was laid out on the floor blood coming from his arm. She had knocked him down after stabbing him in the arm with the pen. Nurses surrounded him helping up and out of the room. Strong arms were wrapped around her waist. She struggled to escape but she couldn't.<p>

Snake Eyes held her tightly as she thrashed about trying to get away. It was a good thing that he decided to watch her for a while. Psyche-Out would be in worst shape if he hadn't. Scarlett had gone from being in a trance to stabbing Psyche-Out with the pen she had. She was screaming the chant that she had said the first time she broke down. She then told Psyche-Out she was going to kill him.

He had moved swiftly from his spot he was hiding in and pulled her off of Psyche-Out. She had stopped thrashing after a while and lay limp in his arms. "I'm sorry…I'm so sorry." She grasped at her hair. He sat her on her feet and she turned around to look at the same ninja that had ruined her mission and knocked her out.

"You're the one who-" she hesitated, unsure of what to say. "This is pitiful." She said to herself backing away from him. "Everything is right there and I can't grasp it. I know who you are. I know that I know, but I can't grasp it. I can't reach it!" she felt helpless and was tired of feeling that way.

The man wear the mask started to make hand gestures toward her and at first she didn't know what he was doing, but she found herself repeating what he was saying to her out loud. "Don't stress over your state right now." She said and he nodded.

"I know Sign Language." she stated more for herself than for him. She looked back just as General Hawk enter the room. She kept her eyes to the floor. She had attacked one of his soldiers. It was almost the same as disobeying.

"Scarlet." He called her and Snake Eyes noticed her very visible flinch.

"Orders are important." She mumbled to herself, while moving to the wall. She stood with her legs apart and her hands braced against the wall. She waited there and Hawk stared. She was expecting him to beat her.

Snake Eyes grabbed her and turning her around to face him. She looked confuse as he quickly signed to her. He was furious but not at her. *Stop. We will not hurt you!* he held her by her wrist. Scarlett stared at him for a long time before acknowledging him.

"But…" She said not sure of herself. "I disobeyed. I-"

*What you did was beyond your control. You cannot be at fault for your actions right now. Don't torture yourself over this. Psyche-Out will be fine.* he calmed her down before she could lose control of her emotions. She nodded slowly.

"Scarlett, do you know how to get back to the bases you were held at?" Hawk was already putting together the team that was going to go.

"Yes." She curiously looked at Snake Eyes' hand grasping her wrist. He let go of her and she looked at Hawk.

"I need you to give me those directions." He said calling a guard to get him a pen. The other one was too bloody. He gave her the pen once the guard had returned. She sat in the chair and started to write. Snake Eyes noticed she was writing with her left hand. He didn't know of any brainwashing technique that would change a person's dominate hand.

Scarlett could tell she was being stared at, so she looked up. *You're right handed.* he signed to her and she looked at her hand. She put the pen in her right hand and continued to write.

"I was not allowed to write with my right hand at all. I had to use my left hand or I would be disobeying an order." She flexed her left hand and then looked up to Hawk. "No one can get in unless they have passed the verification test. The rules that govern that base are much stricter. There are mostly only scientists there that work for Baroness. The base is under her complete control." She handed Hawk the directions. He took them and thanked her.

She had another one of her staring moment but broke it before she was too far gone. "No problem, General." He stared at her now. "Did I say something that was incorrect?" she asked.

"No, nothing at all, I think some of your personality returned to you for a moment." He said to her as he read over the directions. While he did so Scarlett's attention went to Snake Eyes.

Even though she could not remember anyone's name or face she knew his. Well at least his mask. She didn't know what he look like under it. She wasn't sure but she felt a slight fear when she was around him. It was unexplainable and it wasn't fear of bodily harm. She wondered if they didn't get along. She moved back as the fear got worst.

"You will need this to get in." she said showing them the sole of her foot. A large scar was in the middle. "There is an identification tag in my foot. It will pass the verification test, but after you are in, there is no way out but the way you entered. The base is underground. You will have to cut the tag out." She said looking to Hawk.

"How deep is the tag." He asked.

"It will need to be surgically removed." She said putting her foot back on to the floor. "I hope this can be of help to you." She waited for a response.

"One more question. What does this Puppeteer look like?" Hawk asked.

"Puppeteer is 5'5 and 120 lbs. He has black hair and of Russian descent. His eyes are brown and he has a scar on his neck that runs down under his clothes. I gave it to during a relapse with a Ka bar. His laboratory is on the 9th basement level floor. He has an assistant that is by his side almost all the time unless Puppeteer dismisses him. I'm sure he is no threat to you but be careful." She ended up talking to Snake Eyes more than Hawk. He nodded to her.

* * *

><p>Hawk left to prepare the mission. Snake Eyes stay behind for any other use information. He stood listening to Scarlett as she recited every detail of the base that she remembered. He had a vivid idea of what the layout of the base looked like from her description. Scarlett moved to the other side of the room. He could understand why she was afraid of him. A lot of the recruits did the same thing.<p>

"You know me, right?" she asked. He gave her a nod and she continued. "What kind of person am I?" he didn't expect such a question, so it took him a second to reply.

*You're stubborn.* was the first thing that came to him mind.

She looked at him slightly confused. "Me?" she could not see herself being stubborn. Following orders were her priority but she understood wanting to complete something could lead to stubborn behavior.

*Stubborn at times. You're resilient and you have good leadership skills. You can be a soldier at the right time but also light-heart and understanding to your teammates.* she seemed mesmerized by his signing.

"I sound like a good person." Scarlett looked disappointed.

*Why are you disappointed?* he asked.

She shook her head and said "I wonder if I'll ever be that person again. She really does sound well-rounded."

Lifeline enter the room which ended their conversation because Scarlett was about to get a physical exam. Snake Eyes left the room and headed to the briefing room. After a thorough examination and the short surgery on her foot, Scarlett was escorted back to her room. She sat on the bed and waited for the doctor to come. Somehow she fell asleep without realizing it.

* * *

><p><em>Scarlett sat in her room doing her make-up. She didn't dislike make-up. It was just she didn't like putting it on. It was tiresome. She stared at the dark red lipstick and sighed. She normally didn't have to participate in missions like this but the congressman with Cobra affiliations liked red heads. She being the only red head in intelligence automatically volunteered her for the mission. <em>

_She didn't mind using her charm to get information, but she heard stories about the pig she was trying to charm. Not as if he could do any bodily harm to her, she just didn't want to deal with the man. She slipped into her dress that was short and black with a sloping back. Gathering intel was fun, when you got to sneak around but there wasn't any sneaking until later on._

_Pulling on the stilettos, she headed out of her room and met up with Hawk for a quick review. After that she was on her way out. Snake Eyes was on his way in. She stopped him. "Everything went well?" she asked._

_He gave her a nod and looked at her for a minute longer than usual. "I've got to go charm a congressman, Cobra affiliate. It should be an easy in and out job." She looked him over to make sure he wasn't hurt. He looked fine but his attention was still on her._

_*Be careful.* he signed to her quickly and went on his way. _

_Scarlett sighed inwardly. She wasn't angry at him. She was angry at herself. She could never figure out what to say to him. It was frustrating to her that she couldn't get him to talk to her more. She should be satisfied with what little he did, but she wasn't. She hurried to the elevator._

"_Ugh." Scarlett moaned. She rolled over off her side on to her stomach and pushed herself up slowly. Shaking her head she got to her feet. She staggered backwards but caught her balance. She was unsure of what happened. She went through the events of the night, while surveying her surroundings. She was in the congressman's house still in his living room._

_She looked down as she felt something running down her stomach under her dress. She touched her dress and looked at the blood on her fingertips. She remembered what happen. He shot her. Congressman Bridges had received a phone call and when he came back he shot her while her back was turned. She didn't expect him to have an ounce of honor, but she thought he would at least wait until she was facing him. _

_She could hear herself struggling to breathe. She wondered if the bullet hit her lung. She couldn't breathe properly. She moved slowly through the house. She had to get out as quickly as possible. She didn't hear anything else at the moment but she couldn't take any chances. She grabbed for the knife she had between her thighs, surprised it was still there. _

_Her wheezing got louder as she moved through the house. She slowed her pace and stayed to the wall. She could hear footsteps upstairs and yelling that was incoherent. She had to get out of there before she fainted from blood loss. She stopped and slid down the wall her back was pressed against. She took a quick peep around the corner. She could see nothing but black boots coming toward her. She tightened her grip on the knife and tried to slow her breathing so she wasn't wheezing so much. She could hear the foot fall come closer._

_Sudden, she was grabbed up and she turned in her attacker grasp with knife in hand. She was surprised to see Snake Eyes. He took the knife from her and quickly silenced the person who was coming around the corner. Scarlett's wheezing became even louder. _

_Snake Eyes checked her over and found were she was wounded. He ripped open the side of her dress open and examined the wound. It wasn't as bad as it looked but because she couldn't get any oxygen she was in danger. He picked her up quickly and moved them out of the opening. _

"_How did… (wheezing) you-" she took a moment to rest. Then she took a shallow breath of air. "Here so…fast" her body shook as she tried to intake air. Snake Eyes laid her on the floor and then he checked her back seeing that the bullet went through completely. He wasn't ignoring her but he couldn't sign to her and tend to her steadily bleeding wound._

"_I found the infor…mation, but…someone-" she wheezed and her breathing got shallower. "Is it bad?" she asked. He made a sharp sign at her to be quiet. She did so; she was using too much strength trying to talk. After a couple of minutes she could breath. He was wrapping a bandage tightly around her ribs. _

_*You were only supposed to take two hours. You didn't get to your extraction point in time. Hawk was then informed that your cover was blown. He sent us to retrieve you.* he didn't state the fact he left before General Hawk even gave the order._

"_Let me guess. Congressman Bridges called in as many Cobra reinforcements as he could." She stifled a moan as he put her over his shoulder. He picked up the Uzi he had laid on the floor and handed her the semi-automatic pistol he got off the bodyguard he killed. "Thanks for saving me." she checked the gun making sure it was ok. He gave her a quick pat on the back of her thighs. She smiled to herself knowing she really shouldn't be happy at a time like this._

_He left out the room he had ducked into with her over his shoulder._

* * *

><p>Shade open her eyes as the Synapse Drive finally kicked over to secondary power. She sat up and scanned her surroundings. She was in an infirmary room. She noticed the camera and looked down at the hospital gown she wore. She received her orders earlier. She had to escape this place and return to Puppeteer. She stood and went to the door intent on leaving.<p>

"Excuse me, I think I tore my stitches." She said with feinted worry in her voice.

* * *

><p>AN: I hope everyone enjoys this chapter. I know Scarlett's a lot more serious in the new continuity but I just wanted to add just a bit of light-heartedness to her and I do believe she is slightly stubborn. (She wouldn't give Snake Eyes up for her own life, though that counts as love as well) I hope her personality is ok so far; the same goes for Snake Eyes. Aloof characters are really hard for me to portray, so please bear with me as I try my best.<p>

Again this is an AU because there is no way I could figure out when this story can take place, sorry. Actually had to ask my brother what the name of the gun was the Snake Eyes has on almost every cover for his comic. Uzi. I knew of it but had never seen a picture. Very special thanks go to bronwynn for answering all my questions. I hope to continue asking you lots of questions if you're not bugged by it. Another special thanks to Hinotoriai, my beta, who is uninterested in GI Joe but proofread it for me anyway. (that what sister are for) The rating has gone down because I decided not to go the route I was planning to. Review if you want.

Unfortunately school has started, meaning expect infrequent updates. (Although I never stick to a schedule.) I have limited myself to only typing 2,500 words per chapter so I won't overwhelm my beta. So future chapters will be shorter.

~.^ ^.~


	3. Reminiscence

III. Reminiscence

Sweaty hands tightly gripped a hot steering wheel, holding the vehicle steady. Labored breathing was the only other sound than the loud engine of the Humvee. Green eyes focused on the road ahead rather than the things she was leaving behind. She had escaped from the pit but had sustained an injury in her thigh.

Her mind raced as she tried to put together a plan. She had to return to Puppeteer but she wasn't sure how. His base was far away and there was no way for her to find a way there without some type of currency. She glanced at her thigh. The bleed had ceased but she was still feeling the effects of blood loss. She shook her head to clear the fog but nothing seemed to help. She pulled over, knowing that the others would be after her, but she needed to rest or she wasn't going to be able to continue.

She lied back as much as she could and close her eyes trying to rest, so her mind could clear. Drifting slowly asleep her mind went to that man, the one who wore the mask. Shade knew him. She knew him and she didn't understand why. She shouldn't remember anything. She knew she wasn't the person she was supposed to be but she had to follow the orders given. That was what she was made to do. There was no questioning of one's existence. She started to fade into consciousness with the weight of her situation on her mind.

* * *

><p><em>Scarlett opened her eyes to the infirmary room. She looked around slightly annoyed by the tube down her throat. She moved slightly only to feel someone grasping her hand. She twisted her head to see who it was. Snake Eyes was holding her hand. Her chest hurt went she breathed and her ribs felt like someone had kicked her in them, but she was smiling like an idiot.<em>

_She tightened her grip on his hand and he woke up. He slowly sat up from leaning on the side of her bed and looked up at her. Oddly he wasn't wearing his mask. He leaned back so she couldn't see his face but she pulled at his hand and shook her hand. He hesitated but gave in and returned to her side. He laid his head against her thigh looked up at her. _

_Completely forgetting about the tube she tried to talk and gagged instead. She felt her cheeks redden at her blunder. She slid her hand away from Snake Eyes who was a little reluctant to let go. She thought for a second then signed. *What happened?*_

_*Bridges poisoned you during your dinner. It didn't take effect until after we had escaped. It paralyzed your lungs* he took her hand in his again. She had been in a coma for a week after they returned and he stayed with her, fearing she would never awaken. Her green eyes were smiling at him. *What?*_

_She tried not to smile with the tube down her throat but it was hard. She was happy to wake up with him there. *I'm happy you're here with me.* her grasp on his hand returned after she signed. _

_Staring at one another for a long period of time was not an ideal pass time, but it was nice. They didn't need to say anything to one another to know they were content at that moment. She felt herself drifting off to sleep. Slightly afraid she wouldn't awake again heart monitor jumped showing her anxiety._

_Snake Eyes took her hand and held it tightly signing with his other hand to calm down. *You will wake again, and I'll be here waiting.* he watched as she slowly drifted and fought a little to stay awake. Once she was sleep he laid his head back on the side of her and rested his eyes. He hadn't slept in two days because she had two instance of heart failure before she had awoken. He thought he would lose her, something he could not allow to happen, ever._

* * *

><p>Confusion was what always accompanied her dreams. She could never even remember when such events occurred. She understood why and yet she yearned to know who she was. Her mind was always giving her tidbits of information from the past. It disturbed her. She wanted to go back to that life. Shade wanted to be Scarlett. She didn't want to obey anymore. She didn't want to live as a mindless soldier. She wanted to be the woman who was a leader and a friend, not the shell that couldn't move without orders.<p>

The Synapse Drive already began to try and silence her questioning mind. She found no use in fighting, it was futile to resist. She opened her eyes to the inside of the hot and humid Humvee. She hadn't bothered to turn on the air conditioner. It was no use. It was damaged somehow in her escape from the Pit.

She sat up straight and looked out at her environment, a dessert. She had no memory of how she got to the Pit or why she even knew the name. It was just there in the depths of her mind. She turned on the Humvee and got back on to the road. She had to return to base but she wasn't sure why she was going any longer.

To help him… or to obey orders. Her mind was unclear on many things, but one thing was for sure. She was going to end it, everything once she got there. She was just unsure what she was ending. Her hands shook as she held the wheel and her heart pounded as she thought of the many possibilities. None of them seem worth anything. Uncertain of her position she pressed ahead, determined figure out what she wanted. What she really wanted to do.

* * *

><p>The inside of the Cobra base was different from anything Snake Eyes had witnessed. Everything had a sterile feeling to it. Clean. Many scientists moved through the corridors and offices doing whatever it were that they did. He traveled stealthily through the base in search of the Puppeteer. He was on the correct floor but there was no sign of him yet. He found a spot to wait.<p>

He didn't have much time before the guard realized that Scarlett had not returned. Her tag easily let him in but he wasn't sure if he be able to get out so easily without blowing something up.

A door opened into the laboratory and a man in his mid-thirties entered. His appearance was an exact match to what Scarlett had described. Puppeteer moved through his base going over to his computer to check on Shade's whereabouts. "She still has not returned!" he started to pace but stop and looked at his assistance that had just entered. "Leave! I need time to think."

As the assistance left Snake Eyes moved in slowly, he wouldn't kill the man, but he would hurt him.

* * *

><p>She could feel her sweat traveling down her back. The back out gown she wore was sticking to her skin and making her drive even more uncomfortable. She was still in the dessert. It was her third time pulling over but she needed to take a break. Her leg wound was bleeding again. She undid the bandage and cleaned the wound. Then she redid the bandage and took a look at the map. She didn't have much longer until she reached the town.<p>

She stepped out of the vehicle. She looked out at the dessert. Miles and miles of sand lay before her. Shade smiled lightly to herself, her mind wandering off into thoughts she never examined fully. She suddenly heard a noise and looked behind herself. She saw that the other Joes were catching up to her. She had stood there thinking so long she didn't even notice time slip away.

"I'm scared." She said out loud to herself. She didn't move as the Humvee stopped and Duke got out. He was armed but he held his hands up. She didn't trust him, but she knew she had to go back because if she went back to the puppeteer she would never be Scarlett.

"Scarlett, I don't want to hurt you, but you need to give up and return to the pit." He didn't move any closer. Her green eyes had no emotion in them. They were flat and dull. "Scarlett."

"I don't want to be like this anymore…" she looked back to the scenery of the hot dessert. She was tired of the thoughts that laid right before her but she was unable to reach them. "Duke. I'm not going to go back with you yet." She leaned against the SUV. "Not yet." She wanted to stand there with her freedom for a little longer. This person she was now wasn't Scarlett or the puppet that obey order unquestioningly. She was a woman who was lost and felt trapped wherever she was. She didn't feel like she was anyone. She didn't have an identity.

Duke didn't move from his spot, instead he let her stand there watching the scenery.

"Who am I?" she looked down at her thigh noticing that once again it was bleeding. "I can't go back yet…" she hated looking at the faces there knowing them but not really knowing them. She became wary of how Duke was moving in on her. "You'll force me to attack. I have to follow the orders. I can't be captured again. The device will enter a higher setting, believing that I allowed you to capture me. I don't want to lose myself again." She said desperately, knowing the device would take away her control leaving her nothing but a shell once more.

"Scarlett. We'll find a way to get that thing out of you." He tried to assure her. She looked at Duke. They had been close at one time but now she didn't feel that way. He was just a friend. He wanted more from her, to be with her again. She sensed it for a while but she tried to ignore it hoping he would never make the move to tell her. Her heart belonged to someone else. She wondered why she knew that, her memories were surfacing. So many thoughts that made no sense then thoughts she could not even understand. She wondered but knew the answer wouldn't be given. It was never that easy.

"You sound like a good friend. I'm sorry I don't remember you." She lied. She'd rather keep him at a distance. He was pushy at times and she could not deal with too much stress at the moment. Her mind was finally clear but she wasn't sure for how long. "Take me back while I'm still in control."

* * *

><p>Snake Eyes returned with his team. He dropped the prison off at the brig and then went to report to Hawk. When he reached the General's office he was not expecting to see Duke. He was giving Hawk a report but he had taken a beaten. "We have her in the brig at this-" before the words left his mouth Snake Eyes left the room.<p>

He had to get to her. She couldn't be allowed to meet him. He read over some of the research notes on his way back. If she was in contact with him, he could control her easily. He sprinted to the brig and opened the door the guard laid on his back knocked out.

"Kill him." The scientist was already awake and giving a mindless Scarlett orders. She attacked him from above which he easily avoided by tossing her back. She came back on her feet without any delay. Her attacks were coordinate but not effective enough to do any damage. As she attacked she started to become hesitant, until she stopped completely. She shook lightly.

"No." Scarlett shook her head as if she could clear it by doing so. The sound of her blood rushing through her ears was deafening. She moved away from Snake Eyes. She continued to fight the device that willed her to attack. "Get it out… take it out!" she screamed and turned her angry on the small man who had cause her so much pain.

Before she could step forward to the man she felt her grip on her conscious slip. She knew it wasn't because she fainted but because Snake Eyes had knocked her out.

* * *

><p><em>Scarlett sat reading over an encoded message. She didn't have much work left before she was finished for the day. She yawned and stretched. Only ten minutes left before she could go for some training. She stared at the clock and then back to the message. She usually did her training in the morning, but today she didn't.<em>

_She stood and left her workstation. She wandered through the base. She wasn't sure where she was going but she continued to walk. Her path took her to the infirmary. She could hear a heart monitor as if it was right beside her. She turned her head to the sound but it stopped. The silence was deafening only the sound of her breathing. _

_No one was around just her in a desolated infirmary. Her footsteps were slow and unsure as she came to a room that was locked. She touched the cold steel door and realized she was dreaming when she looked into the small window. _

_There was nothing but darkness. It was a void that seem to call to her. It was calming but it was also frightening. She stepped back and looked behind herself. She was alone and the atmosphere was cold. It was just like the white room that she was locked in. A room made especially for torturing that was where she was._

_No longer in the safety of the Pit but in the room she was broken. Words would not form in her mind so she could cry out. Everything was bleak once more. She could see herself drawing images that would pass through her mind. She could hear herself chanting the same thing over and over. _

_Scarlett knew she was dreaming yet she felt like she was in those places again. It was like she was watching herself. All the things that happen to her play out in front of her. She was the bystander but she still could feel the pain. _

_A puppet stood over her laughing as it moved mechanically. It's voice was loud and echoed. It was giving her orders. It was telling her what she had to do. Scarlett shook her head and tried to move away but she couldn't. She couldn't remove herself from the scene that played out. _

_As quickly as it came, it was gone and she was now watching the monster take away something precious, something that could not be replaced. She couldn't move. She couldn't do anything but watch. Watch how she broke apart mentally. She wanted to prove to someone she was strong and wouldn't hold them back. She wanted that person to know her feeling wouldn't interfere with her mission. She wanted to be his partner, his back up. She wanted to be more. _

_Tears streamed down her cheeks as she realized what she had done. She was foolish. She wanted too much. She lost too much because she was too stubborn. She could have gotten out but she pressed on. She didn't leave the base when she was specifically told to. She had disobeyed Hawk's order and she was captured._

_She remembered everything now, from the moment she was captured to the moment she lost all control of herself and became a slave to Cobra. She made the wrong choice. She didn't listen because she was there for her own reasons; not for the team, to prove something that didn't to be proved. He knew she was a strong person he had told her, so why hadn't she listened?_

* * *

><p>A loud grasp for air stopped everyone in the operation room. Scarlett opened her eyes and screamed out in mental anguish. Doc leaned down so she could see his face.<p>

"Scarlett everything is okay, but right now you're in surgery and you can't move. We're almost done. If you can just relax for a little while longer well be done. Okay?" he watched her reaction. She closed her eyes but tears still leaked down her cheeks. The nurse had to put Scarlett under again. Doc sighed relieved he didn't have to deal with a confuse patient.

"Let's finish this up." He said stitching her back up. Puppeteer stood off to the side with cuffs on and Duke behind him with a gun to his head just in case anything went wrong and Scarlett had complications.

* * *

><p>After an hour Scarlett woke up in a room. Her back hurt and she was on her stomach. Slightly confused she looked around and was stopped before she tried to get up. The hand gentle coaxed her to remain on the bed. She turned her head and was looking at Snake Eyes. He was sitting beside the bed.<p>

"I guess I didn't get back before you and I really wanted that money too." She joked but Snake Eyes didn't laugh or acknowledge the joke. He was angry at her. She tried to shrink into the bed but he took her hand and she felt even guiltier. Tears streamed her cheeks as her voice trembled, "I'm sorry. I messed up…I messed up bad."

* * *

><p>AN: Its weird to just stop like this. I'm so use to writing 4,000 to 5,000 words that this awkward for me. The dream sequence is supposed to be confusing. Scarlett has her memories back and knows what happen. I'll explain what happened on her mission later. If anyone has any idea how I can make this story better let me know. I love input. This is not the end for the Puppeteer or his torture of Scarlett he'll be back later, unfortunately. Review if you want.<p>

~.^ ^.~


	4. Persistent

Persistent

Snake Eyes was furious with Scarlett. She had put herself in danger for no reason at all. Her stubbornness almost caused her, her life. He couldn't understand her thought process for that situation. He looked her directly in the eyes.

She was quickly unnerve and tried to avoid looking at him. *Why did you ignore Hawk's orders." He asked signed to her slowly enough for her to understand. He knew if he went any faster she be confused because she was still drowsy. Scarlett sighed lightly as she felt her guilt consume her. Her mind raced with excuse but she had none that would be sufficient enough to explain.

"I thought I could finish getting the information in time." She lied out of fear and she could tell he didn't believe her. She tried to get up but he kept her from doing so. His hand was on her lower back with enough pressure to keep her from getting up. She wanted to escape the conversation so badly.

She stopped trying. *The truth Scarlett.* she wanted to look away from him to hid her shame but she didn't. It would come off as if she was ignoring him when she wasn't.

"I wanted to complete the mission. I had to." She once again tried to sit up.

*Stop.* he pressed her back to the bed. She bit her lip and sighed in pain. His grip lightened significantly when he realized she was in pain.

"I wanted to prove to you…" she stopped mid-sentence and sat up against the protest of Snake Eyes. She completely ignored the pain in her back. "Where is he? Puppeteer, He can't be left alone!" she was panicking.

*He is in the brig. You need to calm down.* he gently touched her shoulder, which causes her to attack him. Her eyes widen as she realized she had just hit him. She didn't understand what was wrong with her. She didn't understand why she felt so afraid, why her heart was pounding.

"I'm sorry, I didn't mean to." She nearly fell off the bed backwards trying to get away. He grabbed her arm to prevent her from hitting the floor.

She didn't understand why she had hit him. She just panicked and struck back. "Something is wrong." Her eyes were wide as she tried to calm down but failed. Her breathing became labored.

*Breath Scarlett. You need to stay in control.* he realized she was having an anxiety attack. He took her hands in one of his and made her look at him. *Breath* he signed letting go her hand for a moment.

Scarlet did as told and controlled her breathing until she was calm again. "I'm stronger than this." She said to herself. She looked at Snake Eyes and sighed. "I wanted you to see that I was still dependable. Silly, right?" she lower her head some and let go of his hands. "I'm always here doing intelligence, I never get to… I feel like I'm not good enough to help you anymore…"

"I was being childish for a change. I don't even know when I got to that point. I didn't like the way I was but I continued. When I went on that mission I realized the extent of my jealousy. I could have said no but I was stubborn and wanted to prove something I didn't have to. I knew that, but still." She looked up at him briefly then back to the bed.

"I was tortured…but it wasn't like anything I have ever experienced. I broke but there wasn't any information they wanted from me. He just wanted to break me, so I was susceptible to that device." she kept her head down. "I wanted to die there… so I wouldn't have to face you."

He didn't fully understand why she was so reckless, nor did he understand her jealously. Overall, what really bothered him was the shame she felt and that it was to the point she rather die than face him. She knew him well enough to know he would never judge her or belittle her for failure. Scarlett was a strong person and something like embarrassment from failure wasn't something that would normally affect her, unless the torture she faced had affected her so badly.

*What did he do to you?* he signed slowly so that she would understand the seriousness. He wanted an answer from her. He needed to know what she had to endure. He needed to know the humiliation she faced. He needed to know why she wanted to die rather than face him again. *Tell me Scarlett.* he grabbed her hands again after he signed. Her eyes were full of fear as if she was reliving the moment that broke her.

* * *

><p><em>She couldn't breathe. The freezing water burned her nose and throat as she inhaled. She didn't want to but she could stop. She needed air. She needed to breathe. Her gasping was loud to her ears. She could hear voices speaking incoherently and laughter. Her hands struggled in the restraints. <em>

_Again the cold water covered face. She cried out in vain as she struggled to hold her breath. The water soaked the towel over her face and once the water was poured again she was desperately trying to hold her breath._

_She tried to sleep but she couldn't. The room was too hot. She could barely breathe. She lay in a corner of the room huddle trying to escape the room through her mind but each thought would bring her back to the room. The noises and the constant sound of dripping water grated on her nerves. She shook lightly as she started to laugh. Hysterical laughter escaped from the deep recesses of her soul. She was breaking down and she wanted to escape the nightmare._

* * *

><p>Her hands grasped at her hair as she blinked away the disturbing memories. Snake Eyes was still by her side. She looked up at him and then quickly away. She was embarrassed by her weakness. "I broke after he…" her hand went to her lower abdomen. She didn't finish. She couldn't. Psyche-Out was entering the room. Snake Eyes stood and looked at Scarlet. She could tell he was worried over her by his posture. It was protective.<p>

"I'm okay… really." She assured him but she was sure he didn't believe her. She didn't believe herself. He left reluctantly. Scarlett looked at Psyche-Out and spotted his arm. "I'm sorry…" she turned her back to him as he took a seat. She didn't want to talk, but it was the only way for her to get out of the infirmary.

Hawk wouldn't let her back on duty for a while. Maybe light duty at best. She was thrilled at that but she didn't want to leave the Pit either. She didn't feel safe outside. She knew it would be a long conversation ahead of her with him. Well, until he got to a topic she wasn't ready to broach.

"Scarlett its okay the situation was out of your control." He finally said once he was situated in a comfortable position. "How are you?"

She smiled to herself knowing everything he was going to say. "I'm tired." She said at first then she continued. "My back is killing me and I just got all my memories back good and bad. How do you think I feel?" She shook her head in shame. "I'm sorry, I feel tired and as if the world is about to collapse on me."

Psyche-Out noticed that her shoulders were shaking. "Scarlett?" he called her lightly. She sniffled and then once again shook her head.

"Can you really help me?" she asked with a broken voice. "I don't like this feeling I have. It hurts…"

"I can't undo what happened to you but I can help you cope with this and deal with it better than you could on your own." He said making sure she understood what he was telling her.

"That is better than nothing…" she looked at her hands and then to Psyche-Out. "He had me…humiliated and-"

* * *

><p>Snake Eyes confined himself to room for the safety of the man in the brig. He didn't trust his self-control at the moment. He stayed out of ear shot of the session Scarlett was having. He understood that she would tell him when she was ready, but he wanted to know while the man was still in arms reach. He wanted to know what the bastard had done to her. He wanted to know so he could come up with a way to torture the man ten times worse than he had done to Scarlett.<p>

When Scarlett came to he was so angry with her. Her first words a sad attempt at humor. He had almost lost her. She had almost become a shadow of herself. Scarlett had almost disappeared complete and he was the cause of it. He had treated her as if she didn't matter to him but the truth was she did. She mattered too much to him and he didn't want to hurt her. A relationship with him would be impossible. She deserved better, she deserved someone who could at least be seen with her without a mask.

He would do anything for her but he had treated her cold. She thought she had become useless because of it. She believed he thought she was inferior to Helix. It wasn't true they were two completely different women on two opposite ends of a spectrum.

Scarlett was something special, someone he cared deeply for. Helix was a comrade. Someone he worked with, yet Scarlett admitted she felt jealous. In any other situation, he assumed it would be endearing that she cared for him that much, but she had let her feelings control her and she ended up hurting herself.

They would find time to talk and clear the air, but for now he just wanted her to get better.

* * *

><p>AN: Sorry for any mistakes, I read over it but after re-reading your work so many times you don't noticed some mistakes and for some reason I hate reading over my work after I finish. I do so anyway. Let me know what you think about this chapter. Only a couple of more chapters left to go, yay! I know it's going to be short but for my word count and the amount of chapters I have I'm doing pretty well. Again I'm sorry for the slow updates. Midterms are upon me :( Sorry for the short chapter as well, I had it laying around and didn't want to add anything else to it so I went ahead and finished it.<p>

~.^^.~


	5. Assistance

V. Assistance

_Scarlett easily downloaded the data without being notice. Her timing was well within her limit. It really was going to be an easy mission, not that she was complaining. She felt good that she could accomplish her mission without a problem. She also felt like some of her old self had come back. She actually felt like she was accomplishing something. Although she enjoyed her job in intelligence she felt useless lately. It wasn't like her to feel weak or insecure but she did. _

_The reason she even took the mission was because of her need to prove to herself that she wasn't useless, that she could still be a good soldier. She wanted to feel like she had helped. She wanted to show everyone she hadn't grown soft sitting behind a desk but that wasn't the only reason and she found it hard to admit the real reason._

_She had seen them working together, Helix and Snake Eyes. They worked so well together that she became jealous and it shocked her because she wasn't that kind of person. She became doubtful of herself and she felt like she was losing something. It was as if her place by his side was threatened, so she jumped at the chance to prove her worth. They were no longer as close as they used to be and she didn't know how to close the distance between them. Her feeling for him didn't seem matter. He was colder to her and she couldn't figure out why. At one point she felt like the rift between them had closed but she now it had reopened and they both stood as opposite ends of a chasm._

_Hawk had asked her if she was sure and she was. She had doubted herself early on, wondering if she was really ready. Now she could smile to herself knowing that the mission was a breeze and there was no need for her to worry. Everything was fine._

_She was wrong, very wrong. She received the call through her comm link almost thirty minutes in to the mission. Hawk had informed her that the mission was sabotaged and she was ordered to leave through the extraction point immediately. _

_She turned to leave the console. The employees seem to be in an uproar for some reason but she couldn't worry over that. She needed to leave and fast, but she hesitated. The download was almost complete. If she only waited a little longer she could escape with the data they needed. She could prove that she was still strong and dependable. _

_She stared back at the computer and wondered vaguely over her inaction. Her reasons for remaining there was less than noble. Selfish reasons that she didn't understand and she didn't want to understand. Was this really her? She shook her head. She didn't need to prove herself to anyone. She knew she was good enough, yet her feet wouldn't move. She stood still and waited. Hawk asked repeatedly for her position. She didn't answer at first but finally did._

_"I'm still waiting for the download. We need this information and this is the only way to get it. I'm on my way after this." she said watching as the vipers started to inspect the employees at the far end of the room. She had 30 percent left to download and the vipers were moving fast._

_"Scarlett you need to get out now. This is an order. Scarlett!" Hawk's voice boomed over the comm link. She snapped out of her thoughts and the download was complete. She grabbed the small drive and headed the opposite way of the inspecting vipers. The facility was easy to navigate. The white walls and mirror floors gave the place a sterile feeling that she hated. The air was cold and she found it odd that she even noticed. She raced down the halls to the extraction point. There was an underground railway that she could use to get to the extraction point but it would be closed soon. If there were any threats detected, the facility was shut down completely until the culprit was found._

_She stopped behind a wall in another hallway as vipers passed. So far from the information she downloaded, there was a facility dedicated to Cobra Scientists. It was under the control of someone name the Conductor. There was no other information about the owner. She also had the location but she needed to get out of the base and back to the pit if the information was going to be of any use._

_She took one of the freight elevators down to the lower sectors where she could reach the railways. Tension was building up in her shoulders as she moved with stealth through the large open area to the tunnel. It would lead her to the extraction point. She was almost there, but she didn't celebrate yet. She needed to be on the helicopter far away from the base before she even started to relax._

_Her comm link had already been turned off by the electromagnetic field that was erected to prevent any incoming or outgoing messages._

_As she moved to the railway she realized her mistake. She had underestimated the time it would take to close the railways. The railways were a tunnel system that was used for transporting weapons and other items. It had security doors all the way through each tunnel that closed when the base was on lockdown. Once closed those doors could not be override by anyone other than a high-ranking Cobra Viper. She went over to the control panel._

_It was simple and she could easily hack it, but Scarlett wasn't even allowed to touch the panel. It had a fatal amount of electricity running through it. She didn't waste time inspecting it. She needed an escape route so she started to survey her surroundings. _

_"No way out." her thoughts were voiced out loud by a man. She turned around only to see a large amount of Cobra soldiers, all of their guns aiming for her. The man who had voiced her thoughts was unknown to her. She had no information on the person who stood in front of her. _

_She had no weapon but it didn't mean she was going down without a fight. She readied herself but only received a light chuckle from the blond haired man. He was well dressed and didn't look like any of the other higher ups she had seen in the base._

_"There will be no fight." He said as he smiled at her, he continued, "You've already lost this battle the moment you came here. He walked away without saying anything else. Scarlett wonder for a split second why no one had fired on her but her question was answered when the floor she stood on was electrified. She blacked out before she realized what happened._

_Hours later she came to strapped to a medical bed. She wasn't panicking but instead looking for a way out. It didn't take her long to realize she was naked and in a room with glass windows on all sides. Still she was fearless. She would show no fear nor would she break under the pressure. It was a promise she made to herself and her family._

_"Hello Scarlett or should I say Shana." her heart leaped to her throat as fear gripped her. If they knew her named they could find her family. When she became a Joe she always knew her family was safe. She never doubted it because she was dead to them no one would learn her real name unless they knew her before becoming a Joe. The world thought Shana 'O Hara was dead, it was only way that a member of the Joes, families could stay safe._

_She couldn't hide the fear that crossed her face in that split second._

* * *

><p>Scarlett came to standing in the communication room of the Pit. She couldn't remember how she had got there or what she had done. She stepped back from the computer and looked around. The room was empty and it was late at night. She could tell a message was sent but it was sent off the grid. She couldn't retrieve it.<p>

She tried to calm down but the only thing that she could remember was speaking to Psyche Out and after they spoke she left. She remembered the week after the session but everything was completely blank after that. She didn't even know what the date was.

She panicked. She lost a large space of time in her memories and she sent a message out to someone. She quickly left the room and ran in one of the guards that did rounds around the Pit at night. He passed her as if nothing was wrong.

"Hey, um… When did I go in to the communication room? How long has it been?" she asked the man and he stopped.

"About an hour or two, you said you were doing some work." He said wondering why she was asking him such an odd question.

"I must have lost track of time, thank you." she said leaving the guard. Her heart pounded in her chest as she felt fear grip her. Everything was blank, no memories at all. She stopped and looked back at the guard who made his way down the hall. She needed to tell someone what happened. She turned and headed to General Hawk's room but stopped midway.

Scarlett grabbed her chest and gasped out in pain. The room was spinning and her heart was pounding irregularly. She dropped to her knees and tried to keep conscious but she couldn't. She felt like she was losing control. She should have been fine. The device was removed. There was nothing else in her body that was foreign. She should have been safe but she wasn't.

She didn't feel like she was herself anymore. Reality was slipping from her grasp and it scared her. She desperately wanted to call out for help but she couldn't. Her mouth wouldn't obey her mind. Her last thoughts terrified her. She had a mission to complete.

Green eyes opened to stare up at a ceiling. She took a deep breath and stood. It was time to start her mission. The command was given and she was to obey. Everything over the last week was in preparation for this moment. She would not fail. She walked quickly down the hallway toward the brig. Her mission was clear and she had no qualms in fulfilling it. She was a shade after all, nothing but a puppet that moved when given the order.

Shade let a smile grace her lips as she entered the brig. She easily took down the guard by charming him and using chloroform. Entering the room was also quite easy for her, since the guard also had the key card. She opened the door to the Puppeteer's room and stepped inside. The short man seemed to be happy to see her.

"It about time you came Shade. Did those fools truly think they could out smart me?" He said as she undid the cuffs on his wrist. She stood back and waited for him to stand. "What are you waiting for, lead the way out!"

"You will not be escaping from this base with me. The Conductor wanted me to relay this message to you. 'Luka Azarov you have out lived your usefulness, I wish you would have listen to me. You have created such a wonderful doll and I believe that I am much better at control it. Please do not think poorly of me, but you have failed Cobra and you know what must be done. Goodbye my friend.' That is the end of the Conductor's message. Goodnight Puppeteer." Shade said as she pulled the combat knife out and the man known as Luka eyes widen in horror. The puppeteer's screams went unheard in the soundproof room.

Shade stepped out of the room dropping the knife and picking up the firearm of the guard she had knockout. She made her way to the elevator that led out of the Pit. As she neared the elevator, alarms began to sound. She assumed that the guard had finally awoken, but it didn't matter at all. She was already on her way out of the Pit. Her mission would not be a failure again. Again an uncharacteristic smile graced her usual expressionless face.

Outside of the Pit, Shade moved quickly toward the Humvee that waited for her a few miles away. She got in and nodded to the driver.

"Did you relay the message to our dear friend?" the man known as the Conductor asked. Shade nodded once more. Inside Scarlett was screaming for help, but outside Shade listened to her new commander and owner. Everything was falling apart once more for Scarlett.

* * *

><p>AN: I have no idea what happened here. I was headed for the ending of the story and ended up throwing in another problem. Ugh… I'm so sorry. This was supposed to be the flashback chapter with the mending of Scarlett and Snake Eyes relationship. It just didn't happen, well the mending part didn't. I am so sorry. I'll get there I promise. Well at least puppeteer's dead. More shall be explained later on the week that Shade use to set up her escape. I am also sorry for the long absence but I been busy with other stories and I didn't want to rush this one out. Please review and let me know what you think and if I have any mistake. I read over it at midnight so I might have missed something. Reviews are encouragements.<p>

~.^ ^.~


	6. Normalcy

AN: Well I decided add AU to the summary so no one else will be confused. I hope everyone already realized that this was AU from the very first AN in chapter one. It was brought to my attention in four reviews (now deleted) I don't know anything about this couple, characters were Ooc and I made up history.

I'm willing to admit, I don't know anything about this couple, but it was clearly said in the first chapter that I didn't. I also said it was AU (so I can make things up since it does not follow canon) and I apologized for the Out of Character in the **first Authors Note**.

Anyhow the AU in the summary should fix this. Thank for reading and I'm very sorry for the abrupt ending.

* * *

><p>Normal<p>

Scarlett was in perfect form as she performed her push-ups. Her mind was clear and she was counting without thinking. She could feel sweat dripping from her nose as she continued. Seven weeks had passed since she was had returned to the Pit. She had gotten back into the swing of things relatively easy.

She finished her last push-up and stood. After doing a couple of stretches she started jogging. Seven weeks since she escaped from the underground base and it was destroyed. She remembered every single day from the moment she returned. The alternative personality was completely gone. No more blackouts or confusion. She was back to herself or as much as she could be.

Physical Training ended and she headed to the showers. The alternative personality that was forced upon her had actually worked to help her. Shade had offered her help to take down the base. She escaped the Pit and faked her loyalty to the Conductor. It was an intelligent plan that General Hawk agreed upon.

After she sent out encoded information on the layout of the base and the guards shifts he sent in his best to retrieve her and destroy the base. It was like clockwork and Scarlett could only remember waking up after the sound of explosion. After that point she didn't have any more interference from the personality, it was gone. Scarlett was confused but she met up with Snake Eyes and Helix to complete the mission. The whole episode felt like it was from a bad dream.

She left the showers after cleaning up. Passing two other Joes on her way to her quarters she gave a greeting and kept on heading to her room.

She had explained her silly reason to Snake Eyes and received what she could only call a lecture of some sort. He was so angry with her she could barely follow the swift signs he had made when he was signing to her.

After a while he had to just leave. She assumed he had no words for her, which she didn't mind. She had no real words to explain her stupidity during those moments. She had let emotions get in the way and caused a lot of troubles.

They talked to one another again after that and she had to promise him she would never do anything so stupid again. He didn't quite believe her but he let the matter rest after a couple of days. It wasn't quite the makeup she wanted but she was satisfied for the time being. There were plenty of things that she didn't tell him, not because she didn't want to. But she wasn't ready to. She would one day but not anytime soon.

She finished dressing in her quarters and then headed to her workstation area. She had a lot of work lately but she had to admit it was better to stay busy. No time was allowed to dwell on mistakes. Busying herself with the day's workload she forgot about her train of thought.

It was finally a normal day for Scarlett.

* * *

><p>AN II: I really did enjoyed writing this story at first. I wish everyone was in character and I could read every comic so I could learn the characters, but that's impossible and that's okay.<p>

Again thank you for reading and the reviews; they encouraged me to write this story that was completely out of my norm. And I really thought it was okay for my first try. If it seems I am just ending this because of a few bad reviews, it not. It's because I don't want to go on and I don't think this story is good, (so maybe alittle because of the reviews) but mostly because of the writer's block. The ending should have been in 5th chapter and I messed that up thinking I should have gone on. I'll probably change it one day to the true ending I wanted, but for now this is the end.

Anyway this is it for me and this fandom. I'm no good at it anyway.


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